<p>The hydrochemical composition of water in the Three Gorges Reservoir area (TGA) has undergone alterations due to eutrophication and human activities, evolving into a weakly alkaline Ca²⁺-rich environment. These changes have profound implications for the saturated permeability coefficient (<i>k</i>_sat) of soils along the reservoir banks, particularly under fluctuating water levels. To investigate these effects, laboratory experiments were conducted using remolded soil specimens from TGA. A weakly alkaline Ca²⁺ solution, formulated as an equivalent ionic solution (EIS), was employed instead of natural river water. The results revealed the evolution of <i>k</i>_sat over time when specimens were immersed in EIS. Initially, <i>k</i>_sat increased slowly, followed by a more rapid rise before eventually stabilizing. Notably, specimens immersed in EIS exhibited higher permeability coefficients compared to those submerged in deionized water (DW) for the same duration. However, the time required to reach peak permeability coefficient was longer in EIS than in DW. This phenomenon can be attributed to the interaction between the EIS and clay particles, which reduces the diffuse double layers (DDL) of the soil accompanying a reaggregate of the dispersed clay particles and quasi-crystallize. Furthermore, cracks formed during air-drying significantly increases permeability, the reduced spacing between clay mineral layers hindered crack healing, leading to greater damage accumulation during wetting cycles with EIS following air-drying. After 11 wetting–drying cycles, the permeability coefficient in the EIS environment increased by approximately 40 times. This study underscores the critical role of interactions between a weakly alkaline Ca²⁺ solution and clay minerals in altering soil permeability.</p>